Table 1. Cryo-EM data collection, refinement, and validation statistics.
| HER2/HER4/NRG1β(EMDB: EMD-41886)(PDB: 8U4L) | HER2/HER4/BTC(EMDB: EMD-41885)(PDB: 8U4K) | HER4/NRG1β(EMDB: EMD-41883)(PDB: 8U4I) | HER4/BTC(EMDB: EMD:41884)(PDB: 8U4J) | |
|---|---|---|---|---|
| Data collection and processing | ||||
| Magnification | 105000 x | 105000 x | 105000 x | 105000 x |
| Voltage (kV) | 300 | 300 | 300 | 300 |
| Electron exposure (e–/Å2) | 45.8 | 45.8 | 68.7 | 45.8 |
| Defocus range (μm) | 0.9–2.0 | 0.9–2.0 | 0.9–2.0 | 0.9–2.0 |
| Pixel size (Å) | 0.835 | 0.835 | 0.835 | 0.835 |
| Symmetry imposed | C1 | C1 | C1 | C1 |
| Initial particle images (no.) | 2938077 | 2261526 | 1264991 | 1715894 |
| Final particle images (no.) | 289192 | 148541 | 205726 | 274540 |
| Map resolution (Å) FSC threshold |
3.3 0.143 |
4.3 0.143 |
3.4 0.143 |
3.7 0.143 |
| Map resolution range (Å) | 3–7 | 3–7 | 3–7 | 3–7 |
| Refinement | ||||
| Initial model used (PDB code) | 7MN5, 3U7U | 7MN5, 3U7U, AF-P35070-F1 | 3U7U | 3U7U, AF-P35070-F1 |
| Model resolution (Å) FSC threshold |
3.5 0.5 |
4.4 0.5 |
3.6 0.5 |
3.9 0.5 |
| Map sharpening B factor (Å2) | –85 | –162.4 | –105.5 | –135.8 |
| Model composition Non-hydrogen atoms Protein residues Ligands |
9989 1230 35 |
9989 1228 35 |
10842 1301 57 |
10851 1297 58 |
|
B factors (Å2) Protein Ligand |
70.49 150.01 |
239.03 398.81 |
70.81 140.13 |
166.67 330.96 |
| R.m.s. deviations Bond lengths (Å) Bond angles (°) |
0.012 1.614 |
0.012 1.697 |
0.012 1.635 |
0.012 1.598 |
| Validation MolProbity score Clash score Poor rotamers (%) |
0.78 0.93 0.09 |
1.04 0.93 0.19 |
0.71 0.62 0.35 |
0.81 0.81 0.17 |
| Ramachandran plot Favored (%) Allowed (%) Disallowed (%) |
98.02 1.98 0 |
96.20 3.80 0 |
97.97 2.03 0 |
97.74 2.26 0 |